[gmx-users] Molecule contains no atoms

[Justin Lemkul]

On 9/6/19 11:13 AM, Tanos Franca wrote:
> Dear users,
> GROMACS 5.1.4 is returning the error message below after running grompp
> with stpr.mdp. Does anyone knows how to fix it?
>
> Program gmx grompp, VERSION 5.1.4
> Source code file:
> /home/cuda1/Downloads/gromacs-5.1.4/src/gromacs/gmxpreprocess/topio.c,
> line: 1001
>
> Fatal error:
> Molecule type 'MOL' contains no atoms
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors

Your topology is somehow formatted incorrectly such that grompp cannot 
find any atoms in it.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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